title: A unified proteochemometric model for prediction of inhibition of cytochrome p450 isoforms.
abstract: A unified proteochemometric (PCM) model for the prediction of the ability of drug-like chemicals to inhibit five major drug metabolizing CYP isoforms (i.e. CYP1A2, CYP2C9, CYP2C19, CYP2D6 and CYP3A4) was created and made publicly available under the Bioclipse Decision Support open source system at www.cyp450model.org. In regards to the proteochemometric modeling we represented the chemical compounds by molecular signature descriptors and the CYP-isoforms by alignment-independent description of composition and transition of amino acid properties of their protein primary sequences. The entire training dataset contained 63 391 interactions and the best PCM model was obtained using signature descriptors of height 1, 2 and 3 and inducing the model with a support vector machine. The model showed excellent predictive ability with internal AUC = 0.923 and an external AUC = 0.940, as evaluated on a large external dataset. The advantage of PCM models is their extensibility making it possible to extend our model for new CYP isoforms and polymorphic CYP forms. A key benefit of PCM is that all proteins are confined in one single model, which makes it generally more stable and predictive as compared with single target models. The inclusion of the model in Bioclipse Decision Support makes it possible to make virtual instantaneous predictions (∼100 ms per prediction) while interactively drawing or modifying chemical structures in the Bioclipse chemical structure editor.
authors.affiliation: Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden.
authors.forename: Maris
authors.initials: M
authors.lastname: Lapins
authors.forename: Apilak
authors.initials: A
authors.lastname: Worachartcheewan
authors.forename: Ola
authors.initials: O
authors.lastname: Spjuth
authors.forename: Valentin
authors.initials: V
authors.lastname: Georgiev
authors.forename: Virapong
authors.initials: V
authors.lastname: Prachayasittikul
authors.forename: Chanin
authors.initials: C
authors.lastname: Nantasenamat
authors.forename: Jarl E S
authors.initials: JE
authors.lastname: Wikberg
mesh_terms: D019540:Area Under Curve; D065607:Cytochrome P-450 Enzyme Inhibitors; D003577:Cytochrome P-450 Enzyme System / Q000378:metabolism; D007527:Isoenzymes / Q000037:antagonists & inhibitors* / Q000378:metabolism; D008956:Models, Chemical; D010599:Pharmacokinetics; D060388:Support Vector Machine
chemical_list: D065607:Cytochrome P-450 Enzyme Inhibitors; D007527:Isoenzymes; D003577:Cytochrome P-450 Enzyme System